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<TITLE>A Powerful Clone Overlap Test for Restriction Fragment Mapping</TITLE>
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<B> Next:</B> <A NAME=tex2html6 HREF="node1.html"> Introduction</A>
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 <H1>A Powerful Clone Overlap Test for Restriction Fragment Mapping</H1>
<P><STRONG> 
Brendan Mumey<BR> <BR> 
 Department of Computer Science<BR> 
 University of Washington, Seattle, WA 98195, USA<BR> 
 <tt> brendan@cs.washington.edu </tt><BR> <BR> 
 Key words: physical mapping, statistical inference,<BR> 
 probabilistic reasoning, cluster analysis
</STRONG><P>
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<H3>Abstract:</H3>
<EM>This paper addresses a computational biology problem which
is to decide whether two clones (segments of a genome)
overlap based on their <em> multiple complete digest</em> (MCD) fingerprint.
The problem arises in the context of building a physical map
of a genome, an important step in the human genome project.
The main result is an overlap test which is
argued to be powerful in a stochastic model of the process
in the sense of admitting the lowest false negative rate for a given rate
of false positives.  Initial experiments show that it yields about
20% fewer false negatives for a given rate of false positives than
a commonly used test.  This is likely to improve the success of
the subsequent mapping stages.
</EM><P>
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<UL> 
<LI> <A NAME=tex2html7 HREF="node1.html#SECTION00010000000000000000"> Introduction</A>
<LI> <A NAME=tex2html8 HREF="node2.html#SECTION00020000000000000000"> A Stochastic Model of MCD Fingerprinting</A>
<LI> <A NAME=tex2html9 HREF="node3.html#SECTION00030000000000000000"> The  a posteriori Probability of Overlap</A>
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<LI> <A NAME=tex2html10 HREF="node4.html#SECTION00031000000000000000"> Estimating </A>
<LI> <A NAME=tex2html11 HREF="node5.html#SECTION00032000000000000000"> Estimating </A>
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<LI> <A NAME=tex2html12 HREF="node6.html#SECTION00040000000000000000"> The Proposed Overlap Test</A>
<LI> <A NAME=tex2html13 HREF="node7.html#SECTION00050000000000000000"> Comparison with a Currently Used Test</A>
<LI> <A NAME=tex2html14 HREF="node8.html#SECTION00060000000000000000"> Open problems and future work</A>
<LI> <A NAME=tex2html15 HREF="node9.html#SECTION00070000000000000000">References</A>
<LI> <A NAME=tex2html16 HREF="node10.html#SECTION00080000000000000000"> Proof of Lemma 1</A>
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<LI> <A NAME=tex2html17 HREF="node11.html#SECTION00081000000000000000"> An Initial Inequality</A>
<LI> <A NAME=tex2html18 HREF="node12.html#SECTION00082000000000000000"> Bounds on </A>
<LI> <A NAME=tex2html19 HREF="node13.html#SECTION00083000000000000000"> Discrepancy between  and </A>
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<LI> <A NAME=tex2html20 HREF="node14.html#SECTION00090000000000000000">   About this document ... </A>
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<P><ADDRESS>
<I>Brendan Mumey <BR>
Mon Aug 12 16:18:30 PDT 1996</I>
</ADDRESS>
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